@jbrowse/core 1.5.3 → 1.5.7

package/assemblyManager/assembly.js

@@ -1,23 +1,23 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = assemblyFactory;
+exports["default"] = assemblyFactory;
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _slicedToArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
 
-var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
+var _objectWithoutProperties2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectWithoutProperties.js"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _toConsumableArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+var _objectSpread2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
 var _jsonStableStringify = _interopRequireDefault(require("json-stable-stringify"));
 
@@ -32,11 +32,6 @@ var _util = require("../util");
 var _QuickLRU = _interopRequireDefault(require("../util/QuickLRU"));
 
 var _excluded = ["signal", "statusCallback"];
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
-
 // Based on the UCSC Genome Browser chromosome color palette:
 // https://github.com/ucscGenomeBrowser/kent/blob/a50ed53aff81d6fb3e34e6913ce18578292bc24e/src/hg/inc/chromColors.h
 // Some colors darkened to have at least a 3:1 contrast ratio on a white
@@ -64,9 +59,9 @@ function loadRefNameMap(_x, _x2, _x3, _x4) {
 
 
 function _loadRefNameMap() {
-  _loadRefNameMap = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(assembly, adapterConf, options, signal) {
+  _loadRefNameMap = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee4(assembly, adapterConf, options, signal) {
     var sessionId, refNames, refNameAliases, refNameMap, reversed;
-    return _regenerator.default.wrap(function _callee4$(_context4) {
+    return _index["default"].wrap(function _callee4$(_context4) {
       while (1) {
         switch (_context4.prev = _context4.next) {
           case 0:
@@ -81,7 +76,7 @@ function _loadRefNameMap() {
 
           case 3:
             _context4.next = 5;
-            return assembly.rpcManager.call(sessionId, 'CoreGetRefNames', _objectSpread({
+            return assembly.rpcManager.call(sessionId, 'CoreGetRefNames', (0, _objectSpread2["default"])({
               adapterConfig: adapterConf,
               signal: signal
             }, options), {
@@ -106,7 +101,7 @@ function _loadRefNameMap() {
             })); // make the reversed map too
 
             reversed = Object.fromEntries(Object.entries(refNameMap).map(function (_ref2) {
-              var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
+              var _ref3 = (0, _slicedToArray2["default"])(_ref2, 2),
                   canonicalName = _ref3[0],
                   adapterName = _ref3[1];
 
@@ -134,23 +129,23 @@ function checkRefName(refName) {
 }
 
 function getAdapterId(adapterConf) {
-  return (0, _jsonStableStringify.default)(adapterConf);
+  return (0, _jsonStableStringify["default"])(adapterConf);
 }
 
 function assemblyFactory(assemblyConfigType, pluginManager) {
-  var adapterLoads = new _abortablePromiseCache.default({
-    cache: new _QuickLRU.default({
+  var adapterLoads = new _abortablePromiseCache["default"]({
+    cache: new _QuickLRU["default"]({
       maxSize: 1000
     }),
     fill: function fill(args, abortSignal, statusCallback) {
-      return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+      return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
         var adapterConf, self, options;
-        return _regenerator.default.wrap(function _callee$(_context) {
+        return _index["default"].wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
                 adapterConf = args.adapterConf, self = args.self, options = args.options;
-                return _context.abrupt("return", loadRefNameMap(self, adapterConf, _objectSpread(_objectSpread({}, options), {}, {
+                return _context.abrupt("return", loadRefNameMap(self, adapterConf, (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, options), {}, {
                   statusCallback: statusCallback
                 }), abortSignal));
 
@@ -165,7 +160,7 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
   });
   return _mobxStateTree.types.model({
     configuration: _mobxStateTree.types.safeReference(assemblyConfigType)
-  }).volatile(function () {
+  })["volatile"](function () {
     return {
       error: undefined,
       regions: undefined,
@@ -191,7 +186,7 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       },
 
       get allAliases() {
-        return [this.name].concat((0, _toConsumableArray2.default)(this.aliases));
+        return [this.name].concat((0, _toConsumableArray2["default"])(this.aliases));
       },
 
       get refNames() {
@@ -289,7 +284,7 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       getAdapterMapEntry: function getAdapterMapEntry(adapterConf, options) {
         var signal = options.signal,
             statusCallback = options.statusCallback,
-            rest = (0, _objectWithoutProperties2.default)(options, _excluded);
+            rest = (0, _objectWithoutProperties2["default"])(options, _excluded);
 
         if (!options.sessionId) {
           throw new Error('sessionId is required');
@@ -311,9 +306,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       getRefNameMapForAdapter: function getRefNameMapForAdapter(adapterConf, opts) {
         var _this = this;
 
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+        return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2() {
           var map;
-          return _regenerator.default.wrap(function _callee2$(_context2) {
+          return _index["default"].wrap(function _callee2$(_context2) {
             while (1) {
               switch (_context2.prev = _context2.next) {
                 case 0:
@@ -347,9 +342,9 @@ function assemblyFactory(assemblyConfigType, pluginManager) {
       getReverseRefNameMapForAdapter: function getReverseRefNameMapForAdapter(adapterConf, opts) {
         var _this2 = this;
 
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+        return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3() {
           var map;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
+          return _index["default"].wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
                 case 0:
@@ -403,9 +398,9 @@ function loadAssemblyReaction(_x5, _x6) {
 }
 
 function _loadAssemblyReaction() {
-  _loadAssemblyReaction = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(props, signal) {
+  _loadAssemblyReaction = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee5(props, signal) {
     var sequenceAdapterConfig, assemblyName, refNameAliasesAdapterConfig, cytobandAdapterConfig, pluginManager, adapterRegions, adapterRegionsWithAssembly, refNameAliases, aliases, cytobands;
-    return _regenerator.default.wrap(function _callee5$(_context5) {
+    return _index["default"].wrap(function _callee5$(_context5) {
       while (1) {
         switch (_context5.prev = _context5.next) {
           case 0:
@@ -425,7 +420,7 @@ function _loadAssemblyReaction() {
             adapterRegions = _context5.sent;
             adapterRegionsWithAssembly = adapterRegions.map(function (adapterRegion) {
               checkRefName(adapterRegion.refName);
-              return _objectSpread(_objectSpread({}, adapterRegion), {}, {
+              return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, adapterRegion), {}, {
                 assemblyName: assemblyName
               });
             });
@@ -473,11 +468,11 @@ function getRefNameAliases(_x7, _x8, _x9) {
 }
 
 function _getRefNameAliases() {
-  _getRefNameAliases = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(config, pluginManager, signal) {
+  _getRefNameAliases = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee6(config, pluginManager, signal) {
     var _type$getAdapterClass;
 
     var type, CLASS, adapter;
-    return _regenerator.default.wrap(function _callee6$(_context6) {
+    return _index["default"].wrap(function _callee6$(_context6) {
       while (1) {
         switch (_context6.prev = _context6.next) {
           case 0:
@@ -507,9 +502,9 @@ function getCytobands(_x10, _x11) {
 }
 
 function _getCytobands() {
-  _getCytobands = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(config, pluginManager) {
+  _getCytobands = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee7(config, pluginManager) {
     var type, CLASS, adapter;
-    return _regenerator.default.wrap(function _callee7$(_context7) {
+    return _index["default"].wrap(function _callee7$(_context7) {
       while (1) {
         switch (_context7.prev = _context7.next) {
           case 0:
@@ -538,9 +533,9 @@ function getAssemblyRegions(_x12, _x13, _x14) {
 }
 
 function _getAssemblyRegions() {
-  _getAssemblyRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(config, pluginManager, signal) {
+  _getAssemblyRegions = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee8(config, pluginManager, signal) {
     var type, CLASS, adapter;
-    return _regenerator.default.wrap(function _callee8$(_context8) {
+    return _index["default"].wrap(function _callee8$(_context8) {
       while (1) {
         switch (_context8.prev = _context8.next) {
           case 0:

package/assemblyManager/assemblyConfigSchema.js

@@ -3,7 +3,7 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = void 0;
+exports["default"] = void 0;
 
 var _configuration = require("../configuration");
 
@@ -64,4 +64,4 @@ var _default = function _default(pluginManager) {
   });
 };
 
-exports.default = _default;
+exports["default"] = _default;

package/assemblyManager/assemblyManager.js

@@ -1,17 +1,19 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = assemblyManagerFactory;
+exports["default"] = assemblyManagerFactory;
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _index = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+var _createForOfIteratorHelper2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/createForOfIteratorHelper.js"));
+
+var _toConsumableArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
 
 var _mobx = require("mobx");
 
@@ -23,14 +25,8 @@ var _configuration = require("../configuration");
 
 var _assembly = _interopRequireDefault(require("./assembly"));
 
-function _createForOfIteratorHelper(o, allowArrayLike) { var it = typeof Symbol !== "undefined" && o[Symbol.iterator] || o["@@iterator"]; if (!it) { if (Array.isArray(o) || (it = _unsupportedIterableToArray(o)) || allowArrayLike && o && typeof o.length === "number") { if (it) o = it; var i = 0; var F = function F() {}; return { s: F, n: function n() { if (i >= o.length) return { done: true }; return { done: false, value: o[i++] }; }, e: function e(_e) { throw _e; }, f: F }; } throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method."); } var normalCompletion = true, didErr = false, err; return { s: function s() { it = it.call(o); }, n: function n() { var step = it.next(); normalCompletion = step.done; return step; }, e: function e(_e2) { didErr = true; err = _e2; }, f: function f() { try { if (!normalCompletion && it.return != null) it.return(); } finally { if (didErr) throw err; } } }; }
-
-function _unsupportedIterableToArray(o, minLen) { if (!o) return; if (typeof o === "string") return _arrayLikeToArray(o, minLen); var n = Object.prototype.toString.call(o).slice(8, -1); if (n === "Object" && o.constructor) n = o.constructor.name; if (n === "Map" || n === "Set") return Array.from(o); if (n === "Arguments" || /^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n)) return _arrayLikeToArray(o, minLen); }
-
-function _arrayLikeToArray(arr, len) { if (len == null || len > arr.length) len = arr.length; for (var i = 0, arr2 = new Array(len); i < len; i++) { arr2[i] = arr[i]; } return arr2; }
-
 function assemblyManagerFactory(assemblyConfigType, pluginManager) {
-  var Assembly = (0, _assembly.default)(assemblyConfigType, pluginManager);
+  var Assembly = (0, _assembly["default"])(assemblyConfigType, pluginManager);
   return _mobxStateTree.types.model({
     assemblies: _mobxStateTree.types.array(Assembly)
   }).views(function (self) {
@@ -57,7 +53,7 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
         _getParent$session = _getParent$session === void 0 ? {} : _getParent$session;
         var _getParent$session$se = _getParent$session.sessionAssemblies,
             sessionAssemblies = _getParent$session$se === void 0 ? [] : _getParent$session$se;
-        return [].concat((0, _toConsumableArray2.default)(assemblies), (0, _toConsumableArray2.default)(sessionAssemblies));
+        return [].concat((0, _toConsumableArray2["default"])(assemblies), (0, _toConsumableArray2["default"])(sessionAssemblies));
       },
 
       get rpcManager() {
@@ -71,7 +67,7 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
       get allPossibleRefNames() {
         var refNames = [];
 
-        var _iterator = _createForOfIteratorHelper(self.assemblies),
+        var _iterator = (0, _createForOfIteratorHelper2["default"])(self.assemblies),
             _step;
 
         try {
@@ -99,9 +95,9 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
       // use this method instead of assemblyManager.get(assemblyName)
       // get an assembly with regions loaded
       waitForAssembly: function waitForAssembly(assemblyName) {
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+        return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
           var assembly;
-          return _regenerator.default.wrap(function _callee$(_context) {
+          return _index["default"].wrap(function _callee$(_context) {
             while (1) {
               switch (_context.prev = _context.next) {
                 case 0:
@@ -148,9 +144,9 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
         }))();
       },
       getRefNameMapForAdapter: function getRefNameMapForAdapter(adapterConf, assemblyName, opts) {
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
+        return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee2() {
           var assembly;
-          return _regenerator.default.wrap(function _callee2$(_context2) {
+          return _index["default"].wrap(function _callee2$(_context2) {
             while (1) {
               switch (_context2.prev = _context2.next) {
                 case 0:
@@ -184,9 +180,9 @@ function assemblyManagerFactory(assemblyConfigType, pluginManager) {
         }))();
       },
       getReverseRefNameMapForAdapter: function getReverseRefNameMapForAdapter(adapterConf, assemblyName, opts) {
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
+        return (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee3() {
           var assembly;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
+          return _index["default"].wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
                 case 0:

package/assemblyManager/index.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -8,13 +8,13 @@ Object.defineProperty(exports, "__esModule", {
 Object.defineProperty(exports, "assemblyConfigSchemaFactory", {
   enumerable: true,
   get: function get() {
-    return _assemblyConfigSchema.default;
+    return _assemblyConfigSchema["default"];
   }
 });
 Object.defineProperty(exports, "default", {
   enumerable: true,
   get: function get() {
-    return _assemblyManager.default;
+    return _assemblyManager["default"];
   }
 });
 

package/configuration/configurationSchema.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -8,11 +8,13 @@ Object.defineProperty(exports, "__esModule", {
 exports.ConfigurationReference = ConfigurationReference;
 exports.ConfigurationSchema = ConfigurationSchema;
 
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
+var _defineProperty2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/defineProperty.js"));
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+var _slicedToArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/slicedToArray.js"));
 
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+var _objectSpread2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
+
+var _typeof2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/typeof.js"));
 
 var _mobxStateTree = require("mobx-state-tree");
 
@@ -22,12 +24,8 @@ var _configurationSlot = _interopRequireDefault(require("./configurationSlot"));
 
 var _util = require("./util");
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
-
 function isEmptyObject(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && !Array.isArray(thing) && thing !== null && Object.keys(thing).length === 0;
+  return (0, _typeof2["default"])(thing) === 'object' && !Array.isArray(thing) && thing !== null && Object.keys(thing).length === 0;
 }
 
 function isEmptyArray(thing) {
@@ -47,8 +45,8 @@ function preprocessConfigurationSchemaArguments(modelName, inputSchemaDefinition
   var options = inputOptions;
 
   if (inputOptions.baseConfiguration && inputOptions.baseConfiguration.jbrowseSchemaDefinition) {
-    schemaDefinition = _objectSpread(_objectSpread({}, inputOptions.baseConfiguration.jbrowseSchemaDefinition), schemaDefinition);
-    options = _objectSpread(_objectSpread({}, inputOptions.baseConfiguration.jbrowseSchemaOptions || {}), inputOptions);
+    schemaDefinition = (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, inputOptions.baseConfiguration.jbrowseSchemaDefinition), schemaDefinition);
+    options = (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, inputOptions.baseConfiguration.jbrowseSchemaOptions || {}), inputOptions);
     delete options.baseConfiguration;
   }
 
@@ -100,7 +98,7 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
     }
   };
   Object.entries(schemaDefinition).forEach(function (_ref) {
-    var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
+    var _ref2 = (0, _slicedToArray2["default"])(_ref, 2),
         slotName = _ref2[0],
         slotDefinition = _ref2[1];
 
@@ -110,14 +108,14 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
       modelDefinition[slotName] = slotDefinition;
     } else if (typeof slotDefinition === 'string' || typeof slotDefinition === 'number') {
       volatileConstants[slotName] = slotDefinition;
-    } else if ((0, _typeof2.default)(slotDefinition) === 'object') {
+    } else if ((0, _typeof2["default"])(slotDefinition) === 'object') {
       // this is a slot definition
       if (!slotDefinition.type) {
         throw new Error("no type set for config slot ".concat(modelName, ".").concat(slotName));
       }
 
       try {
-        modelDefinition[slotName] = (0, _configurationSlot.default)(slotName, slotDefinition);
+        modelDefinition[slotName] = (0, _configurationSlot["default"])(slotName, slotDefinition);
       } catch (e) {
         throw new Error("invalid config slot definition for ".concat(modelName, ".").concat(slotName, ": ").concat(e));
       }
@@ -141,7 +139,7 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
   });
 
   if (Object.keys(volatileConstants).length) {
-    completeModel = completeModel.volatile(function
+    completeModel = completeModel["volatile"](function
       /* self */
     () {
       return volatileConstants;
@@ -160,8 +158,8 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
     completeModel = completeModel.extend(options.extend);
   }
 
-  var identifierDefault = identifier ? (0, _defineProperty2.default)({}, identifier, 'placeholderId') : {};
-  var modelDefault = options.explicitlyTyped ? _objectSpread({
+  var identifierDefault = identifier ? (0, _defineProperty2["default"])({}, identifier, 'placeholderId') : {};
+  var modelDefault = options.explicitlyTyped ? (0, _objectSpread2["default"])({
     type: modelName
   }, identifierDefault) : identifierDefault;
   var defaultSnap = (0, _mobxStateTree.getSnapshot)(completeModel.create(modelDefault));
@@ -170,12 +168,12 @@ function makeConfigurationSchemaModel(modelName, schemaDefinition, options) {
     var matchesDefault = true; // let keyCount = 0
 
     for (var _i = 0, _Object$entries = Object.entries(snap); _i < _Object$entries.length; _i++) {
-      var _Object$entries$_i = (0, _slicedToArray2.default)(_Object$entries[_i], 2),
+      var _Object$entries$_i = (0, _slicedToArray2["default"])(_Object$entries[_i], 2),
           key = _Object$entries$_i[0],
           value = _Object$entries$_i[1];
 
       if (matchesDefault) {
-        if ((0, _typeof2.default)(defaultSnap[key]) === 'object' && (0, _typeof2.default)(value) === 'object') {
+        if ((0, _typeof2["default"])(defaultSnap[key]) === 'object' && (0, _typeof2["default"])(value) === 'object') {
           if (JSON.stringify(defaultSnap[key]) !== JSON.stringify(value)) {
             matchesDefault = false;
           }

package/configuration/configurationSlot.js

@@ -1,13 +1,13 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = ConfigSlot;
+exports["default"] = ConfigSlot;
 
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+var _typeof2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/typeof.js"));
 
 var _mobxStateTree = require("mobx-state-tree");
 
@@ -27,7 +27,7 @@ var typeModels = {
   stringArray: _mobxStateTree.types.array(_mobxStateTree.types.string),
   stringArrayMap: _mobxStateTree.types.map(_mobxStateTree.types.array(_mobxStateTree.types.string)),
   numberMap: _mobxStateTree.types.map(_mobxStateTree.types.number),
-  boolean: _mobxStateTree.types.boolean,
+  "boolean": _mobxStateTree.types["boolean"],
   color: _mobxStateTree.types.refinement('Color', _mobxStateTree.types.string, isValidColorString),
   integer: _mobxStateTree.types.integer,
   number: _mobxStateTree.types.number,
@@ -41,7 +41,7 @@ var fallbackDefaults = {
   stringArray: [],
   stringArrayMap: {},
   numberMap: {},
-  boolean: true,
+  "boolean": true,
   color: 'black',
   integer: 1,
   number: 1,
@@ -81,7 +81,7 @@ var typeModelExtensions = {
   fileLocation: objectJSON,
   number: literalJSON,
   integer: literalJSON,
-  boolean: literalJSON,
+  "boolean": literalJSON,
   frozen: objectJSON,
   // special actions for working with stringArray slots
   stringArray: function stringArray(self) {
@@ -118,7 +118,7 @@ var typeModelExtensions = {
           self.value.set(key, val);
         },
         remove: function remove(key) {
-          self.value.delete(key);
+          self.value["delete"](key);
         },
         addToKey: function addToKey(key, val) {
           var ar = self.value.get(key);
@@ -163,7 +163,7 @@ var typeModelExtensions = {
           self.value.set(key, val);
         },
         remove: function remove(key) {
-          self.value.delete(key);
+          self.value["delete"](key);
         }
       }
     };
@@ -218,7 +218,7 @@ function ConfigSlot(slotName, _ref) {
     description: _mobxStateTree.types.literal(description),
     type: _mobxStateTree.types.literal(type),
     value: _mobxStateTree.types.optional(_mobxStateTree.types.union(JexlStringType, model), defaultValue)
-  }).volatile(function () {
+  })["volatile"](function () {
     return {
       contextVariable: contextVariable
     };
@@ -272,14 +272,14 @@ function ConfigSlot(slotName, _ref) {
 
     };
   }).preProcessSnapshot(function (val) {
-    return (0, _typeof2.default)(val) === 'object' && val.name === slotName ? val : {
+    return (0, _typeof2["default"])(val) === 'object' && val.name === slotName ? val : {
       name: slotName,
       description: description,
       type: type,
       value: val
     };
   }).postProcessSnapshot(function (snap) {
-    if ((0, _typeof2.default)(snap.value) === 'object') {
+    if ((0, _typeof2["default"])(snap.value) === 'object') {
       return JSON.stringify(snap.value) !== JSON.stringify(defaultValue) ? snap.value : undefined;
     }
 

package/configuration/configurationSlot.test.js

@@ -1,11 +1,11 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 var _configurationSlot = _interopRequireDefault(require("./configurationSlot"));
 
 test('can convert a string slot to and from a callback', function () {
-  var model = (0, _configurationSlot.default)('tester', {
+  var model = (0, _configurationSlot["default"])('tester', {
     type: 'string',
     defaultValue: 'foo'
   });
@@ -20,7 +20,7 @@ test('can convert a string slot to and from a callback', function () {
   expect(instance.expr.evalSync()).toBe('foo');
 });
 test('can convert a numeric slot to and from a callback', function () {
-  var model = (0, _configurationSlot.default)('tester', {
+  var model = (0, _configurationSlot["default"])('tester', {
     type: 'number',
     defaultValue: 12,
     contextVariable: ['something']
@@ -33,7 +33,7 @@ test('can convert a numeric slot to and from a callback', function () {
   expect(instance.expr.evalSync()).toBe(12);
 });
 test('can convert a stringArray slot to and from a callback', function () {
-  var model = (0, _configurationSlot.default)('tester', {
+  var model = (0, _configurationSlot["default"])('tester', {
     type: 'stringArray',
     defaultValue: ['foo', 'bar']
   });
@@ -48,7 +48,7 @@ test('can convert a stringArray slot to and from a callback', function () {
   expect(instance.value).toEqual(['foo', 'bar']);
 });
 test('can convert a slot with a default function value to a scalar value', function () {
-  var model = (0, _configurationSlot.default)('tester', {
+  var model = (0, _configurationSlot["default"])('tester', {
     type: 'string',
     defaultValue: 'jexl:get(feature,"foo")'
   });

package/configuration/util.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -13,9 +13,9 @@ exports.isConfigurationSchemaType = isConfigurationSchemaType;
 exports.isConfigurationSlotType = isConfigurationSlotType;
 exports.readConfObject = readConfObject;
 
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+var _typeof2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/typeof.js"));
 
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+var _toConsumableArray2 = _interopRequireDefault(require("/data/jbrowse-components2/node_modules/@babel/runtime/helpers/esm/toConsumableArray.js"));
 
 var _mobxStateTree = require("mobx-state-tree");
 
@@ -154,7 +154,7 @@ function getTypeNamesFromExplicitlyTypedUnion(maybeUnionType) {
           throw new Error("invalid config schema type ".concat(type));
         }
 
-        typeNames.push.apply(typeNames, (0, _toConsumableArray2.default)(typeName));
+        typeNames.push.apply(typeNames, (0, _toConsumableArray2["default"])(typeName));
       });
       return typeNames;
     }
@@ -217,5 +217,5 @@ function isConfigurationModel(thing) {
 }
 
 function isConfigurationSlotType(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'isJBrowseConfigurationSlot' in thing;
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'isJBrowseConfigurationSlot' in thing;
 }

package/data_adapters/BaseAdapter.d.ts

@@ -26,12 +26,12 @@ export interface AnyAdapter {
 }
 export declare type AnyDataAdapter = BaseAdapter | BaseFeatureDataAdapter | BaseRefNameAliasAdapter | BaseTextSearchAdapter | RegionsAdapter | SequenceAdapter;
 export declare abstract class BaseAdapter {
+    config: AnyConfigurationModel;
+    getSubAdapter?: getSubAdapterType | undefined;
+    pluginManager?: PluginManager | undefined;
     id: string;
     static capabilities: string[];
-    config: AnyConfigurationModel;
-    getSubAdapter?: getSubAdapterType;
-    pluginManager: PluginManager | undefined;
-    constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    constructor(config?: AnyConfigurationModel, getSubAdapter?: getSubAdapterType | undefined, pluginManager?: PluginManager | undefined);
     /**
      * Called to provide a hint that data tied to a certain region will not be
      * needed for the forseeable future and can be purged from caches, etc